Plastic microchip electrophoresis for genetic screening: the analysis of polymerase chain reactions products of fragile X (CGG)n alleles

Clinical screening of abnormal chromosomes associated with fragile X syndrome (FXS) demands a high-throughput method including DNA sizing and detection of the amplified products. This study is to explore the use of polymer microchip electrophoresis for the analysis of polymerase chain reaction (PCR) products of fragile X (CGG)n alleles to facilitate a fast exclusion test of FXS. The sequences flanking the CGG-repeat of FMR1 gene was amplified by betaine-PCR and the amplified products were desalted and then analyzed by microchips which were fabricated on poly(methyl methacrylate) (PMMA) substrate. The PCR bands with more than six CGG-repeats in difference could be clearly distinguished in less than 3 min by microchip electrophoresis with a separation length of 6 cm. It was found that the signal was greatly enhanced with the use of both covalent (Cy5) and intercalating dye (TORRO-3), which has never been demonstrated before. We tested the method by reanalysis of twelve samples from males and six samples from females. For female samples with less than six repeat differences, Southern blotting method was performed to confirm or exclude the findings from microchips. It was found that the test results from all male and female samples show a 100% correlation between the microchip electrophoresis and the existing methods.     

Restriction Enzyme Pattern Analysis of Mycobacteria DNA by Capillary Electrophoresis with Laser-Induced Fluorescence Detection

A new method for rapidly detecting restriction enzyme patterns of Mycobacterium DNA using capillary electrophoresis with laser-induced fluorescence detection (CE-LIFD) was developed. Polymerase chain reaction was used to amplify a 439-bp fragment of a 65,000-kDa (M _r) heat shock protein gene (hsp65) of Mycobacterium. After digesting amplification products by BstEII and HaeIII, patterns of enzyme cleavage products were detected by both CE-LIFD and agarose gel electrophoresis (AGE), respectively. Experimental parameters of CE were optimized. Restriction enzyme patterns of Mycobacterium DNA were detected in optimum electrophoresis conditions: a coated capillary column with a length of 50 cm and an internal diameter of 100 μm, an electrophoresis buffer of 45 mmol/l Tris-boric acid-ethylenediaminetetraacetic acid, and a running voltage of 11 kV. The restriction enzyme patterns for eight species of mycobacteria were studied. Relative standard deviations of the relative migration times of DNA segments were <3.6%. Compared with AGE, CE is more outstanding in resolution and detection time, and it can be applied as a more effective means to DNA restriction enzyme pattern analysis. Translated from the Chinese Journal of Chromatography, 2005, 23(1) (in Chinese)     

Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions

The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double‐stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polymer with different concentrations and molecular weights (Mws). Migration mechanism of dsRNA during CE was studied by the mobility and resolution length (RL) plots. We found that the RL depended on not only the concentration of HEC, but also the Mw of HEC. For instance, RL of small dsRNA fragment was more influenced by concentration of high Mw HEC than large dsRNA fragment and RL of large dsRNA fragment was more influenced by concentration of low Mw HEC than small dsRNA fragment. In addition, we found electrophoretic evidence that the structure of dsRNA was more compact than dsDNA with the same length. In practice, we succeeded to separate the glyceraldehyde 3‐phosphate dehydrogenase siRNA in the mixture of the siRNA ladder marker within 4 min.     

Fragmentation mechanism for the loss of XCY (X and Y = O,OR, S) from 2-phenyl-1,3,4-oxadiazole-5-one and related sulfur-containing compounds

The fragmentation mechanism for loss of X?C?Y (X and Y = O or S) from 2-phenyl-1-3-4-oxadiazole-5-one and related sulfur-containing compounds begins with the breaking of the C? N bond of the heterocyclic ring. Then a X?C?Y molecule is ejected with the initial formation of a non-rearranged ion. The major part of ΔH_R⁰ is associated with the stabilization of this neutral fragment. The initial fragment ion is further rearranged before it decomposes.     

A simple and precise diagnostic method for spinal muscular atrophy using a quantitative SNP analysis system

A simple and precise diagnostic method for spinal muscular atrophy (SMA) using high‐resolution CE‐based single‐strand conformation polymorphism (CE‐SSCP) was developed in this study. SMA is a common genetic disorder caused by an abnormality in the relative copy numbers of SMN1 and its centromeric copy SMN2, which differ only in two nucleotides, namely at exons 7 and 8. Therefore, the precise discrimination of the differences in sequence as well as their relative quantities is crucial for the diagnosis of SMA. Multiplex ligation‐dependent probe amplification and sequence‐sensitive DNA separation using hydroxyethyl cellulose and hydroxypropyl cellulose blended polymer matrix are currently the available methods used in the diagnosis of SMA. However, these methods are limited by their extended hybridization step and low resolution. In this study, the simultaneous discrimination of SMN exons 7 and 8 was successfully demonstrated using high‐resolution CE‐SSCP. Unlike the previously reported alternative method, single base differing amplicons were baseline‐separated because of its extraordinary resolution, thus providing accurate and precise quantification of each paralog.     

CE Determination of 2-(9-Carbazole)ethyl Chloroformate-Labeled Oligopeptides

A pre-column derivatization method for sensitive determination of oligopeptides, using the tagging reagent 2-(9-carbazole)ethyl chloroformate (CEOC-Cl) followed by capillary electrophoresis (CE) with diode-array detection, has been developed. Maximum yield close to 100% were observed when a three to fourfold molar excess of reagent was used at pH 9.0–10.0. Excess reagent was extracted with n-hexane–ethyl acetate 9:1–10:1 (v/v); this enabled direct analysis using CE with no significant disturbance from the major fluorescent reagent degradation by-products. The effects on the results of buffer pH and of SDS and organic modifier concentrations were examined. Good baseline resolution in the separation of five CEOC-peptides was achieved with a 48.5-cm total length (effective length 40 cm) 50-μm inner diameter capillary column.     

Capillary electrophoresis and phenylboronic acid solid phase extraction for the determination of S‐adenosylmethionine/S‐adenosylhomocysteine ratio in human urine

An approach that allows direct analysis of the ratio of S‐adenosylmethionine (SAM) and S‐adenosylhomocysteine (SAH) by using CE is presented. The analytes were extracted on phenylboronic acid phase and eluted with 100 mmol/L HCl. CE separation of the analytes took place in the transient isotachophoresis mode with addition of NaCl and meglumine to the samples. The sensitivity (S/N = 3) and quantification limit (S/N = 10) of the method were 0.07 and 0.2 μmol/L, respectively, using a silica capillary with 50 μm internal diameter and 30.5 cm total length. The BGE was 0.02 mol/L Tris with 1 mol/L HCOOH (pH 2.2), and the separation voltage was 15–17 kV. Accuracy of SAM and SAH analysis in urine was 96 and 105%, respectively; interday precision for the SAM/SAH ratio was within 6%. The theoretical plate number exceeded a million. Total analysis time was 8.5 min.     

Combining UV photodissociation action spectroscopy with electron transfer dissociation for structure analysis of gas‐phase peptide cation‐radicals

We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas‐phase peptide cation‐radicals produced by electron transfer dissociation. z ‐Type fragment ions ^●Gly‐Gly‐Lys⁺, coordinated to 18‐crown‐6‐ether (CE), are generated, selected by mass and photodissociated in the 200–400 nm region. The UVPD action spectra indicate the presence of valence‐bond isomers differing in the position of the C_α radical defect, (α‐Gly)‐Gly‐Lys⁺(CE), Gly‐(α‐Gly)‐Lys⁺(CE) and Gly‐Gly‐(α‐Lys⁺)(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time‐dependent density functional theory (TD‐DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion‐electron reactions. Specifically, z ‐type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation. Copyright © 2015 John Wiley & Sons, Ltd.     

Comparison of the mechanical properties of styrene‐based ionomers containing either crown ether or pentaethylene glycol with those of underneutralized ionomers

Dynamic mechanical properties of styrene‐based ionomers containing varying amounts of either 15‐crown‐5 ether (CE) or pentaethylene glycol (PG) are compared with those of ionomers of varying degree of neutralization (ND). The cluster T_g (T_g,c) and ionic modulus of the ionomers decrease with increasing amount of CE or PG or decreasing ND. Thus, we propose that the CE binds Na⁺ strongly to form a large‐sized complex. Thus, the electrostatic interactions between charges decrease, leading to lower T_g,c. For the PG‐containing ionomers, the PG acts as polar plasticizer, further lowing the T_g,c. In the case of the underneutralized ionomers, the T_g,c is reduced by the existence of both relatively weak hydrogen bonds between carboxylic acid groups and relatively strong ionic bonds between ion pairs in the multiplets. The small‐angle X‐ray scattering results are also supportive of the above interpretations. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1358–1367     

SN-2-artige massenspektrometrische Fragmentierungen bei substituierten N-Alkylpiperidinen. 10. Mitteilung über das massenspektrometrische Verhalten von Stickstoffverbindungen [1]

An S_N2-type fragmentation was observed on mass spectrometric analysis of N-(ω-X-alkyl)-2-alkylpiperidines (X = NRCOR′,  CONH₂,  COOR,  NH₂). The molecular ion after loss of the 2 alkyl substituent on the piperidine ring may eject the neutral piperideine on attack of the substituent X on the α-carbon of the N-substituted alkyl-chain. Through this process a cyclic fragment ion is formed. The influence of its ring size and of the substituent X on the stability of this fragment was investigated. The S_N2 reaction is favoured in the case of production of five- and six-membered rings.     

Application of gas chromatography–tandem mass spectrometry (GC/MS/MS) for the analysis of deuterium enrichment of water

Incorporation of deuterium from deuterium oxide (²H₂O) into biological components is a commonly used approach in metabolic studies. Determining the dilution of deuterium in the body water (BW) pool can be used to estimate body composition. We describe three sensitive GC/MS/MS methods to measure water enrichment in BW. Samples were reacted with NaOH and U‐¹³C₃‐acetone in an autosampler vial to promote deuterium exchange with U‐¹³C₃‐acetone hydrogens. Headspace injections were made of U‐¹³C₃‐acetone‐saturated air onto a 30‐m DB‐1MS column in electron impact‐mode. Subjects ingested 30 ml ²H₂O, and plasma samples were collected. BW was determined by standard equation. Dual‐energy X‐ray absorptiometry scans were performed to calculate body mass, body volume and bone mineral content. A four‐compartmental model was used to estimate body composition (fat and fat free mass). Full‐scan experiments generated an m/z 45 peak and to a lesser extent an m/z 61 peak. Product fragment ions further monitored included 45 and 46 using selected ion monitoring (Method1), the 61 > 45 and 62 > 46 transition using multiple reaction monitoring (MRM; Method2) and the neutral loss, 62 > 45, transition (Method3). MRM methods were optimized for collision energy (CE) and collision‐induced dissociation (CID) argon gas pressure with 6 eV CE and 1.5 mTorr CID gas being optimal. Method2 was used for final determination of ²H₂O enrichment of subjects because of lower natural background. We have developed a sensitive method to determine ²H₂O enrichment in BW to enable measurement of FM and FFM. Copyright © 2015 John Wiley & Sons, Ltd.     

Analyzing and monitoring of phage–bacteria interaction using CE

The utilization of CE for monitoring bacteria–phage interaction was investigated in this study. Streptococcus thermophilus and Lactobacillus bulgaricus strains and their phages were used as model bacteria and phages for the purpose of validation in this study. CE with heterogeneous polymer polyethylene oxide was utilized for the separation of intact bacteria and investigation of phage–bacteria interaction. An intact phage detection was carried out with CZE by adding SDS in the running buffer. Calibration graphs of bacteria and phages were obtained with R² values of 0.963 and 0.937, respectively. S. thermophilus strain was infected with its virulent phage B3‐X18 for investigation of phage–bacteria interaction. It was observed in capillary electropherogram that the culture was lysed depending on the multiplicity of infection value and it showed to be completely lysed when the multiplicity of infection value was 10. The interaction of S. thermophilus strain with L. bulgaricus phage was also investigated by using a CE and a microbiological method and it was observed that the L. bulgaricus phage attached itself to the cell wall of S. thermophilus strain without damaging the cell.     

Modulation of Serotonin Receptors in Neurodevelopmental Disorders: Focus on 5-HT7 Receptor

Since neurodevelopmental disorders (NDDs) influence more than 3% of children worldwide, there has been intense investigation to understand the etiology of disorders and develop treatments. Although there are drugs such as aripiprazole, risperidone, and lurasidone, these medications are not cures for the disorders and can only help people feel better or alleviate their symptoms. Thus, it is required to discover therapeutic targets in order to find the ultimate treatments of neurodevelopmental disorders. It is suggested that abnormal neuronal morphology in the neurodevelopment process is a main cause of NDDs, in which the serotonergic system is emerging as playing a crucial role. From this point of view, we noticed the correlation between serotonin receptor subtype 7 (5-HT₇R) and NDDs including autism spectrum disorder (ASD), fragile X syndrome (FXS), and Rett syndrome (RTT). 5-HT₇R modulators improved altered behaviors in animal models and also affected neuronal morphology via the 5-HT₇R/G₁₂ signaling pathway. Through the investigation of recent studies, it is suggested that 5-HT₇R could be a potential therapeutic target for the treatment of NDDs.     

Portable capillary electrophoresis system for identification of cattle breeds based on DNA mobility

A portable CE system was developed for the identification of cattle breeds. The system had a width of 44 cm, depth of 27 cm, height of 13 cm, and a weight of only ∼8 kg and included an LIF detector, with everything integrated into a small box. The specific sizes of genes were quickly separated and detected with a high sensitivity based on the difference in the DNA mobility using a diode‐pumped solid‐state LIF detector. Using this system, the 100‐bp DNA ladder was analyzed under a 1.0% PVP (M_r=300 000) sieving gel matrix in a fused silica capillary with LODs of 4.4–13.0 pg/μL (S/N=3) for 100–3000 bp DNAs, which indicates ten times improved value than other commercialized portable CE system. The migration times and the peak areas showed good reproducibilities with relative standard deviations that were less than 0.49 and 1.3% (n=5), respectively. Based on the difference in the DNA mobility of the microsatellite and SNP markers, Korean cattle and Holstein were exactly identified as the model cattle breeds within 32 and 3.5 min, respectively.     

Protein Fractionation of Cowpea (Vigna unguiculata (L.) Walp) Leaf, Flower and Seed by Capillary Electrophoresis and Its Potential for Variety Identification

The proteins of different faction of cowpea [Vigna unguiculata (L.) Walp] were fractionated by capillary electrophoresis (CE). The extracting solvent system was one of the most critical factors in the optimization exercise. To improve reproducibility, seed samples needed to be defatted with chloroform/methanol (V:V=2:1) as preferred prior to protein extraction. Proteins were extracted from seeds, leaves and flowers with 50% aqueous 1‐propanol and separated on a 50 (m×20 cm fused silica capillary column using a UV detector at 200 nm. Separation was conducted at constant voltage (10 kV, 40°C), using iminodiacetic acid (pH 2.5) containing 0.05% hydroxypropylmethylcellulose (HPMC) and 20% acetonitile. The results showed that proteins extracted from all fraction of cowpea were successfully separated by CE in less than 20 min. Seed extracts provided the greatest number of eluted protein peaks, followed by flower and leaf, respectively. The seed‐protein extracts provided unique CE patterns for different varieties; hence the seed was the tissue chosen as being most suitable for variety identification. As a result, an optimized procedure was developed to provide rapid identification of cowpea varieties, based on capillary electrophoregram patterns.     

Detection of S‐adenosylhomocysteine and methylation index in blood by capillary electrophoresis

This work proposes an approach to the direct analysis of S‐adenosylhomocysteine (SAH) and the methylation index in blood using CE with UV detection (CE‐UV). After application of meglumine postinjection, we achieved SAH in‐capillary preconcentration in the HClO₄ extracts of erythrocytes, which improved the detection limit (S/N = 3) of SAH up to 3 fmol or 180 nmol/L at the injection volume of 50 nL, taking into account the sample dilution rate. CE‐UV was carried out in 30 mM glycine and 45 mmol/L HCl (pH ～1.8) at 17 kV in a capillary 48 cm in length and 50 μm id. Accuracy of the technique was 101% and reproducibility was about 12%.     

High‐throughput functional marker assay for detection of Xa/xa and fgr genes in rice (Oryza sativa L.)

We apply CE for high‐throughput analysis of functional markers for marker‐assisted selection in rice. The accuracy, throughput and reproducibility of CE analysis for sequence‐tagged site (STS) and simple sequence repeat (SSR) markers for bacterial blight resistance and aroma genes are demonstrated by using a CE system. Multiplex PCR products displayed well‐differentiated allelic variants using different STS and SSR markers for identification of xa13, Xa21 and fgr genes using the CE system compared to 1.2% agarose gel images. Moreover, consumption of PCR product is much less in the CE system compared to traditional agarose gel systems. Sample consumption is less than 0.1 μL per analysis, thereby conserving samples for further downstream analysis. Out of 29 genotypes in BC₁F₃ generation, 16 plants were found homozygous for all the three genes, viz., xa13, Xa21 and fgr. These homozygous lines can be used as potential donors in rice breeding programmes.     

A Single‐Surface Electrochemical Biosensor for the Detection of DNA Triplet Repeat Expansion

Molecular diagnostics of inherited neurodegenerative disorders such as fragile X syndrome, myotonic dystrophy or Friedreich ataxia (FRDA) is based on analysis of the length of trinucleotide repetitive sequences in certain loci of genomic DNA. The current methods employ PCR and electrophoretic determination of the amplified DNA fragment size. We have recently shown that length of a triplet repetitive DNA sequence can be determined using a double‐surface electrochemical technique involving multiple hybridization of the expanded triplet repeat with short labeled reporter probe (spanning several trinucleotides). Here we propose a single‐surface sensor employing an analogous principle. Target DNA (tDNA) is adsorbed onto surface of a carbon (pyrolytic graphite or screen‐printed) electrode. Biotin‐labeled reporter probe (RP) is hybridized with the immobilized tDNA followed by binding of streptavidin‐alkaline phosphatase (ALP) conjugate. The ALP catalyzes production of an electroactive indicator (1‐naphthol) which is detected voltammetrically on the same electrode. Signal resulting from this electrochemical enzyme‐linked DNA hybridization assay is normalized to the amount of tDNA immobilized at the transducer surface either by measuring intrinsic tDNA voltammetric response, or using electrochemical labeling of the tDNA with osmium tetroxide 2,2′‐bipyridine complex. Detection of (GAA)_n?(TTC)_n triplet repeat expansion in nanogram quantities of PCR‐amplified tDNAs, including amplicons of patients' genomic DNA, is demonstrated. We show that our technique allow differentiation between normal and pathological alleles of X25 gene related to the FRDA.     

Universal fluorescent multiplex PCR and capillary electrophoresis for evaluation of gene conversion between SMN1 and SMN2 in spinal muscular atrophy

We have developed a capillary electrophoresis (CE) method with universal fluorescent multiplex PCR to simultaneously detect the SMN1 and SMN2 genes in exons 7 and 8. Spinal muscular atrophy (SMA) is a very frequent inherited disease caused by the absence of the SMN1 gene in approximately 94% of patients. Those patients have deletion of the SMN1 gene or gene conversion between SMN1 and SMN2. However, most methods only focus on the analysis of whole gene deletion, and ignore gene conversion. Simultaneous quantification of SMN1 and SMN2 in exons 7 and 8 is a good strategy for estimating SMN1 deletion or SMN1 to SMN2 gene conversion. This study established a CE separation allowing differentiation of all copy ratios of SMN1 to SMN2 in exons 7 and 8. Among 212 detected individuals, there were 23 SMA patients, 45 carriers, and 144 normal subjects. Three individuals had different ratios of SMN1 to SMN2 in two exons, including an SMA patient having two SMN2 copies in exon 7 but one SMN1 copy in exon 8. This method could provide more information about SMN1 deletion or SMN1 to SMN2 gene conversion for SMA genotyping and diagnosis.     

Fragile X mental retardation protein: past, present and future

We begin by reviewing the first characterization of fragile X syndrome, which ultimately led to cloning of the FMR1 gene. Discovery of the molecular basis of this disorder, including expansion of a trinucleotide repeat, gave insight not only into fragile X syndrome but also into the premutation syndromes. Features of fragile X syndrome are discussed including the patient phenotype down to the neuronal phenotype. The domain features of the fragile X mental retardation protein FMRP are described, as are the mRNAs bound by FMRP and the role of post-translational modifications as regulators of FMRP function. The relatively new role of FMRP in progenitor cells is reviewed, as is FMRP localization in cells and how FMRP is regulated by glutamatergic signaling in the brain. Understanding how metabotropic glutamate receptors impact FMRP has led to novel therapeutic approaches in treating this disorder.